For only the cost of a Fleet Ship Module (same price as a ship slot BTW) you can have a Vor'cha Battle Cruiser with both options. The new ship will have the hull of the better one and the option to switch BO slots between the 2.

All you have to do is not be on red alert. Go to the ship screen where you normally select you BO for chairs and under the 5th slot and a ways you can select which setting you want.

Keep in mind it's not necessary to do it, but it does give more options.

Same thing with the 2 Nova T5 ships
Hull, Sheilds, and Console layout of the Fleet version.
The ability to switch between
Sci Sci Eng Tac Tac
and
Sci Tac Eng Sci Sci

I would love it if the Dev Team would revise the ship system. Given some older ships are now at end-game, it only makes scense to adopt an upgrade / refit program so you can level up the ship you want to.

Starter Ships have an option of being Refitted at Tier 1:

NX gets refitted to the NX-Refit
TOS Consitution gets refitted to the TMP Consitution
The Oberth and the Miranda gets just a general refit.

TMP Consitution gets one last refit to Tier 3.

Galaxy Players can get the option to refit to Dreadnaught (if unlocked) or a General Refit.

The rest get refitted all the way to Tier 5. Those ships with C-store Varients, buying the ship from the store unlocks an additional refit slot for the consoles (which is basically what it is now).

At the same time, Cryptic can go back and think of different traits of making some ships attractive to switch into than staying with the same ship you've been in. Some ships better speed, some have better skill boosts in some areas, some have better accuracy, etc etc.

This is what I would like to be done. It's a more attractive option than the player shipyard becoming rather.....cluttered.

The solution to this is simple:
1) Add a new ship equipment type called "Bridge Module".
2) Have this module control BOFF seating.
3) Have each module tied to a specific set of ships. Lower tier modules could have less restrictions, higher tier (C-Store) modules could have more specific requirements.